Hi everybody,
I have not found any threads answering to my issue.
I sequenced 50 bp reads with Illumina HiSeq.
My FastQC report shows a really good quality (between 32 and 40 along all the sequence) but I can not understand why the first positions of the reads (1 to 16 bp) exhibit worse quality than the end of the reads.
Would you have ideas regarding the cause of this?
I can not say if it is linked, but the first positions also show high percentage of A, compared to C, G and T and then %A/T lines meet as well as %G/C lines.
I have an additional question : what is for you the "threshold" of duplicated reads level between "good" and "bad" sequences?
Thank you very much.
I have not found any threads answering to my issue.
I sequenced 50 bp reads with Illumina HiSeq.
My FastQC report shows a really good quality (between 32 and 40 along all the sequence) but I can not understand why the first positions of the reads (1 to 16 bp) exhibit worse quality than the end of the reads.
Would you have ideas regarding the cause of this?
I can not say if it is linked, but the first positions also show high percentage of A, compared to C, G and T and then %A/T lines meet as well as %G/C lines.
I have an additional question : what is for you the "threshold" of duplicated reads level between "good" and "bad" sequences?
Thank you very much.
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